Blogging the biotechnology revolution

Systems Biology is changing the way biology is done. Is it a fad or is it effective? This blog tracks current happenings and helps you stay on top of the field. You can find a list of relevant papers at systems biology paper watch Have you heard a talk or read a paper in bioinformatics / systems biology you would like to tell other people about? Email: and get the word out!

Thursday, January 05, 2006

PSB 2006
Michael Ashburner, "Ontologies for biologists - A community model for the annotation of genomic data"
One of the originators of the GO ontology, Dr. Ashburner talked about the intial planning and development of the GO ontology and how it (and everything in bioinformatics) should follow the "Manifesto of liberation of bioinformatics":
-Be open source.
-Use open standards.
-Make data and code available without constraint.
-Involve your community.

He also noted that in the near future there will be links between the three main categories in the GO ontology ( meaning there will be interrelationships between molecular functions, biological processes, and locations. For me, this means more headache for developing methods that must utilize the now more complex (interrelated) heirarchy of the ontology. It seems from this talk that the future is more and more ontologies that are all linked together somehow. He mentions that there are many specialized ontologies that are popping up that augment GO. Think things like neuro ontology and ligand ontology (author's ideas not Dr. Ashburner's); moreover these ontologies are linked and launched through efforts like the national center for biomedical ontology.

Perhaps the most successful type of new ontology (well I'll assume it's the most successful because it's the only other one he got into) is Sequence Ontology or (SO). Here sequences are annotated with different features for different locations on the sequence with a defined ontological heirarchy. He mentions attributes encompassing sequence attributes, mutational consequences, and chromosomal variation.
All in all it was an interesting talk about the future of biological ontologies, which, in my view, is a pretty much thankless job but very important to the field. Think over 1000 citations on Scholar.


Blogger Francis Crick said...

Hmm interesting. I hope they are satisfied with maximum accuracy/completeness of the existing data and connections in GO before making more networks beyond the current ones. But I think this is a common critique of systems bio in general...

12:17 PM  
Blogger The Bioinformatics Blog said...

Ya he mentioned that one approach is community annotation, which for the most part he forwned upon. He talked about Gene ontology developers (GODs!) as the main people annotating. This is kind of akin to wikipedia where there are a few people who do most of the annotating.

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